Freesurfer January 2011

freesurfer@nmr.mgh.harvard.edu

99 participants
144 discussions

mkanalysis-sess in Stable 5
by Adam Nitenson 20 Jan '11

20 Jan '11

Hi Freesurfers, I'm trying to update our analysis for Stable 5, and I'm having some trouble trying to recreate our current Stable 4 version (espcially since I have not yet made a gui-less analysis). The command I used was: mkanalysis-sess -analysis fmcsm5_functionals_Stable5 -TR 2 -paradigm paradigm -event-related -funcstem fmcsm5 -motioncor -inorm -polyfit 2 -mcextreg -nconditions 9 -timewindow 24 -prestim 4 -TER 2 -autostimdur However, it's not accepting the -motioncor flag, and I'm not sure what the correct replacement is. For reference, I'm trying to replicate the analysis as close to the original, which has the following analysis.info file: analysis fmcsm5_functionals TR 2.000000 fsd bold funcstem fmcsm5 inorm 100.000000 runlistfile tpexclude parname paradigm designtype event-related nconditions 9 Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 Condition 5 Condition05 Condition 6 Condition06 Condition 7 Condition07 Condition 8 Condition08 Condition 9 Condition09 and analysis.cfg text -extreg mcextreg -nextreg 3 -delay 0.000000 -TER 2.000000 -polyfit 2 -gammafit 2.250000 1.250000 -gammaexp 2.000000 -timewindow 24.000000 -prestim 4.000000 -autostimdur Thank you, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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Beginner Question on registration process
by Gabriele Arnulfo 20 Jan '11

20 Jan '11

Hi all, I'm a new freesurfer user and I've a small question for you all. Which the faster and reliable way to map a list of points into the freesurfer geometrical space? I've already read the pdf/ppt but there's no suggestion in there about which command should be used (if any). I've read about matlab tools that could be used for this purpose is it right? My task is really simple but i cannot figure out which is the best way. I've got a list of points (basically intra-cerebral electrodes coordinates segmented from MRI) in the MRI space and I'd like to calculate the respective points in the freesurfer space. Cheers, gabriele -- In a world without wall, how needs WINDOWS??

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Re: [Freesurfer] How to make a surface overlay? - repost
by Ed Gronenschild 20 Jan '11

20 Jan '11

Hi Bruce, I managed to do what I wanted: by linking the ?.aparc.annot file with ?thickness file and FreeSurferColorLUT.txt I get a list of thickness value, segID and structure name. Now I can change each thickness into whatever value I want and save it as a curve file which I can then overlay on the pial surface. Thank you for your suggestions. Ed On 19 Jan 2011, at 17:31, Bruce Fischl wrote: > it's 'curv' format (read_curv.m I think) > On Wed, 19 Jan 2011, Ed > Gronenschild wrote: > >> What is the format of ?.thickness files? >> >> On 19 Jan 2011, at 15:43, Bruce Fischl wrote: >> >>> read_annotation.m will load a .annot file. We'll try to digup the >>> tksurfer >>> bit that did this >>> >>> >>> On Wed, 19 Jan 2011, Ed >>> Gronenschild wrote: >>> >>>> Hi Bruce, >>>> >>>> I'm not familar with matlab but I can read the matlab scripts to >>>> understand >>>> what they are doing. I can then convert the code into C code. >>>> Which matlab script can I use to load the parcellation? >>>> >>>> My suggestion would be to load the ?.thickness and replace the >>>> thickness >>>> values with the corresponding -log(p) values. However, I don't know >>>> which >>>> thickness in this file belongs to which segID? >>>> >>>> Ed >>>> >>>> On 19 Jan 2011, at 14:28, Bruce Fischl wrote: >>>> >>>>> Hi Ed, >>>>> >>>>> sorry, I keep hoping someone else will respond as we did put >>>>> something >>>>> together to do this once upon a time, but apparently it's faded >>>>> from all >>>>> of our memories. You could do it in matlab by loading the >>>>> parcellation and >>>>> just setting every vertex with the parcellation value to the same >>>>> scalar. >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> >>>>> On Tue, 18 Jan 2011, Ed Gronenschild wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I've done some statistics on thickness and volume >>>>>> of the default cortical regions (segIDs 1000 - 1035 >>>>>> and 2000 - 2035) for a number of subjects. >>>>>> How can I show for instance the p values >>>>>> (expressed as -log(p)) as an overlay on the pial >>>>>> surface of fsaverage? >>>>>> >>>>>> Ed >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to >>>>> whom it is >>>>> addressed. If you believe this e-mail was sent to you in error and >>>>> the e-mail >>>>> contains patient information, please contact the Partners >>>>> Compliance HelpLine at >>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>> you in error >>>>> but does not contain patient information, please contact the >>>>> sender >>>>> and properly >>>>> dispose of the e-mail. >>>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >> >> >>

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error message in mri_concat: fp==0
by Lars M. Rimol 20 Jan '11

20 Jan '11

Hi, I got this error message when attempting to use mri_concat. Number or inputs, frames etc. seems ok, but when it is about to write the output file, this happens: Writing to /home/lmr/test.mgh , -1): could not open file: fp==0 (I use v.4.5.0) Any suggestions? Thank you! yours, LMR -- yours, Dr. Lars M. Rimol

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overlaping in aparc+aseg
by LAOUCHEDI MAKHLOUF 19 Jan '11

19 Jan '11

hi everyone after running recon-all i noticed (on somme normal patients) overlaping in some labels: part of image with 11165 and 11113 wich correspond to p { margin-bottom: 0.21cm; } - ctx_lh_G_front_inf-Orbital p { margin-bottom: 0.21cm; } - ctx_lh_S_orbital-H_Shaped at the same time (verified with fslview) thanks p { margin-bottom: 0.21cm; }

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wmparc.stats file
by Inge Knudson 19 Jan '11

19 Jan '11

I'm wondering what is being quantified in the wmparc.stats files created by recon-all. It appears to be the volume of white matter in a number of different structures, including the subcortical structures. There are also what I assume are white matter volumes for the cortical regions included in the aparc parcellation. Any clarification is appreciated. Thank you.

2 1

longitudinal analysis
by sima chalavi 19 Jan '11

19 Jan '11

Dear Freesurfer experts I have some longitudinal data from tp1 and tp2 for three different groups (A,B,C) and 2 different genders (G1,G2). I followed the longitudinal stream and processed all the images in FS 4.5. For further analysis, I saw the post from Martin and Doug at http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14266.html in which they suggested to first do the mris_preproc for each time point and then calculate the differences using mris_calc. What I did was instead of doing mris_preproc for each tp separately I made a FSGD file and put all the information about our different classes including baseline (BL) and followup (FU), see below, and then run mris_preproc which gives me ?h_thickness_both_tp_fwhm10.mgh files. GroupDescriptorFile 1 Title diagnosis_gender_glmdir MeasurementName thickness Class A_G1_BL Class A_G1_FU Class A_G2_BL Class A_G2_FU Class B_G1_BL Class B_G1_FU Class B_G2_BL Class B_G2_FU Class C_G1_BL Class C_G1_FU Class C_G2_BL Class C_G2_FU After mris_preproc for example I made the following contrast to compare the changes from BL to FU and then I ran mri_glmfit: contrast to compare (A_BL vs C_BL) vs (A_FU vs C_FU): contarst_AvCBLvAvCFU=[1 -1 1 -1 0 0 0 0 -1 1 -1 1] >> mri_glmfit - - y ?h_thickness_both_tp_fwhm10.mgh - - fsgd diagnosis_gender_BL_FU.fsgd - - C contarst_AvCBLvAvCFU.mtx - - surf fsaverage ?h - - cortex - - glmdir glmdir So using this approach I wanted to compare the difference between the 2 tps using the contrasts and not calculating first the differences using mris_calc and then runnig glm. However, I am not sure if I am doing the right thing. Could you please send me your feedbacks. Thanks in advance, Sima Chalavi. -- Sima Chalavi, Ph.D. student King's College London Institute of Psychiatry (IoP) Box P040, De Crespigny Park London SE5 8AF. Tel:+44-2078485702 BCN Neuroimaging Center (NIC) University Medical Center Groningen Antonius Deusinglaan 2 P.O. Box 196 9713 AW Groningen www.neuroimaging-DID.com

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19 Jan '11

Hi surfers: I want to project PET data from a group of subjects in the native space into fsaverage surface. It seems I should use mri_vol2surf. And here I am asked to input register.dat for --srcreg argument. I wonder which register.dat should I use, the register matrix between subject volume data with the fsaverage template? or subject PET with their T1? And how to generate this register.dat. Thanks very much for your help! Jing

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tksurfer display problem
by Chris Watson 19 Jan '11

19 Jan '11

Hi, when trying to look at surfaces in tksurfer, all I see is a small part of the data in the posterior of the brain (see attached for example). There are no errors on the command line when I run tksurfer. This only started happening very recently. Here's some system info: (CentOS 5.5, 64-bit; FreeSurfer v5.0) [freesurfer@occipital TGA]$ uname -a Linux occipital.tch.harvard.edu 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 12:54:20 EST 2010 x86_64 x86_64 x86_64 GNU/Linux [freesurfer@occipital TGA]$ /sbin/lspci | grep -i nv 40:00.0 VGA compatible controller: nVidia Corporation G73GL [Quadro FX 560] (rev a1) I wouldn't think I need to update my graphics card driver. But, does anyone know how to fix this? Thanks, Chris

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Testing installation, recon-all problem
by Tetiana Dadakova 19 Jan '11

19 Jan '11

Dear Freesurfer users, I installed Freesurfer and now I am trying to test the installation. When I type <recon-all -s bert -all>, I get an error <ERROR: you do not have write permission to /Applications/freesurfer/subjects/bert> But actually I do have write permission to this folder. Do you have any idea what can be wrong? Or what else should I check regarding installation to understand where this problem comes from? Thank you for your time, Tetiana.

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Freesurfer January 2011